Skill check mechanics

Ok here is the gist of the game.
There are 6 main areas that take several turns to move between since you need to go through other areas to get to them. The players are trying to manage resources and gain enough power to stop the random villain from achieving his/her goal. The villain is chosen at random before each game. Each has a different win condition.
The game is Co-op and the 6 main areas have 3 card slots each.
Every turn an event will be drawn and goes into the appropriate area moving any cards that are there to the next slot. If a 4th card is added to any location the bad thing on the card that slides off happens with any negative chits that it accumulated due to other actions.
End of every turn an encounter is drawn for the current location of each player.
Some key elements in this game are that characters can advance or decrease in skills though only slightly (margin of 3 better or worse minimum 1) since at some points in the game a character may need to start back from a new character if they died. So to cut death back I have limited advancement to only a few points.

Now I'm trying to think of some mechanics on skill checks etc.
I'm trying to think of some unique way to apply skill checks. The ways I know best are as listed below from other games.
Arkham horror - roll dice equal to skill level and successes on 5-6
Betrayal at House on the Hill - dice have only 0-2 pips per side and you need specific numbers for certain things to happen.
Minion Hunter - Roll a die add the skill to the die roll. Depending if easy, moderate, or hard you get double result, the actual result, or half the result respectively.
Battle Star Galactica - Play cards from your hand with numbers matching skills(colors) associated with the task and get equal to or above the number needed.

I'd like to hear some other ideas keep in mind the characters will have 4-6 skills each and those skills may vary throughout the game.

Also I'm thinking there should be something different to stop the cards on the main areas so players aren't always doing the same thing, but I'd like some ideas if anyone has any.

Do the characters actually need to test skills in this numerical fashion? It sounds like the enemy is going to be really speeding along so maybe the players skills should just be actions they can take to try to interfere with the enemy progress, and by limiting the number of actions they can take per turn you're asking them to 'test' their skill by deciding where to gamble on leaving a threat until the following turn.

Some example ideas (which may or may not be relevant because I can't tell too much about your game):
- A thief or magician character could have a 'Sleight Of Hand' skill that lets him swap the negative chits you mention between different threat cards in his room; he doesn't eliminate a threat but he can influence which is the biggest danger.
- A warrior type could remove up to his current strength in chits from a single threat as long as he doesn't move this turn. If he reduces the chits to 0, the card is removed from the room.

The 'test' for these guys is do I use my skill this turn for a partial benefit or do I wait until next turn when I can get the full benefit but I'm risking a card or encounter that makes things too bad for me to handle?

If you do want to stick with skill checks, any of the methods you mention are perfectly reasonable, just make sure you test them a lot to ensure the level of difficulty is correct. An alternative might be to give players action points which they can spend on their skills for a particular level of efficiency so maybe spend up to 6 action points and then roll 1d6; if you roll equal to or less than the action points spent you succeed. If you limited players to 10 action points per turn this would give them a lot of hard decisions but would also allow them to choose to succeed at critical checks rather than get screwed by the luck of the die.

Actions are a good thing to add so that each character is different. I was thinking of something similar for them so there will be lots of re playability.

For the events I do like the action point idea you gave but I need to think of a way that perhaps more than one card can be removed in a single turn. I'm leaning towards some type of resource gathering through encounters throughout the board then spending resources to eliminate different threats.

The negative chits that are added to cards are added via player discussions of areas. Any time players talk about an area or a strategy and are not on the same space they must place a random negative chit on the card closest to the left with the fewest chits already on them. This is in play to have the game having some knowledge of player plans as long as the players are contacting each other via phone. This is due to wire taps in the game. The players are investigating a city so unless they are in the same area they cannot make any information they find or gain without consequence. The system is still a bit wonky so I might need to make minor changes to it.

There will be encounters that involve skills on the spaces that are not the main spaces. Through these skill checks there will be rewards or sometimes penalties for failing.

Building on the action point idea perhaps have resources worth certain values and you need to roll under the amount of resources you discard. Allowing someone who is not on your space to discard resources and you only getting half the total worth rounded up of the discarded resources added to whatever you and anyone else on your space discards. Then you make a roll on a d10 and need to roll under that number.
I could take it farther and have 3 colors of resources which could signify Physical evidence, Interviews, & Rumors. Each event might be only subject to certain colors. These cards could also have some other effect like maybe one could be worth 4 Yellow but you can additionally spend it to move 3 spaces (normal movement is only 1 space so that could get you to some other threat but that 4 yellow might be really beneficial to someplace another player is.

The feel of the game I'm going for is a horror theme set in the modern day. Some form of conspiracy is happening depending on the villain and win and lose conditions depend on the villain you are against.

not really. In shadows you know what you need like a pair of cards or a straight. In this you know what symbols you need but every turn more add to random locations. It's more gathering resources (cards) and then using them to beat the encounters.
Though I haven't played "Witch of Salem" I put this game on hold until I try it. B/c reading about it a lot of my ideas seemed similar and I want to make sure my game is different enough or else I'll have to scrap it and re define the mechanics.

I do like the color dice option but in this current game I think that's too random since you are supposed to use the resources you have found so far.
I think colored cards work best for this and I've made a bunch of alterations on this game making only 6 spaces in the game as compared to in between locations and took away skills so it's just the cards you have acquired now.

A: Is it going to be a contested roll ( 2 rolls opposing each other) or is it going to be 1 roll vs a target number.

B: How many variables in going to take part of the roll. In a Arkham Horror system, you can influence the roll by changing the number of dice rolled, the target number required to make a hit and the number of hit to succeed. So in a system like this, you can insert 3 different variables.

C: What are the Value ranges? In s system where you roll X dice and add bonus Y, you could end up in a situation where some rolls are impossible or always succeed. For example, it is impossible to roll 12 or more with 1d6+4 while rolling 4D6+8 is an automatic success.

D: Does the amount by which you succeed has an impact on the results. Ex: Exceeding your TN by 5 points gives a bonus effect.

E: Are there going to be situational modifiers that gives bonus/malus or that raise/lower the TN.

Skill checks are good for RPG because you have a lot of options in your hand. So your options are grouped in cathegories matching one of your skills. So, whatever you push, for example, door, window, coffin, statue, etc. would mean a check to your strength. But if you don't have that much options (and many times in board games you don't) maybe generic skills are not necessary.

You could use cards, like with RPG wizards or priest, with things that a certain type of character is supposed to do right. So playing the card means the action outcome is always succesful. The difficulty relies in that many times you don't have the card in your hand at the moment you need it. And many cool action cards would be scarse in your pile.

I didn't get quite well what your game is about, but maybe this will help. Suppose you have a Detective character deck of Actions cards, filled with: Get Clue, Shadow Suspect, Interrogate and others. This are things a Detective is supposed to do, and it won't make much sense if he couldn't do it because dices didn't favor him. Your Conspirator (nemesis) character deck of Actions cards could be: Bribe, Mislead, Vanish, Pass Without Trace, or the like.

Remember, the more you know, the more you mess yourself. Keep thinking!

The action cards deal is similar to what I'm using now in the current prototype. And the events are things happening around the city that will appear at the key locations as of right now they only either progress one or another antagonist. I scaled this game back a bit from my initial wants since mechanically it works better as well. Not to mention it's a coop game that I can't even beat yet as it's written I need to make sure it's able to be won so there will need to be tweaks still.